For atomic frequency standards in which fluctuations of the local oscillator (LO) frequency are the dominant noise source, we examine the role of the the servo algorithm that predicts and corrects these frequency fluctuations. We derive the optimal linear prediction algorithm, showing how to measure the relevant spectral properties of the noise and optimise servo parameters while the standard is running, using only the atomic error signal. We find that, for realistic LO noise spectra, a conventional integrating servo with a properly chosen gain performs nearly as well as the optimal linear predictor. Using simple analytical models and numerical simulations, we establish optimum probe times as a function of clock atom number and of the dominant noise type in the local oscillator. We calculate the resulting LO-dependent scaling of achievable clock stability with atom number for product states as well as for maximally-correlated states.